Data from: A large-scale phylogeny of Amphibia including over 2800 species, and a revised classification of extant frogs, salamanders, and caecilians

The extant amphibians are one of the most diverse radiations of terrestrial vertebrates (>6800 species). Despite much recent focus on their conservation, diversification, and systematics, no previous phylogeny for the group has contained more than 522 species. However, numerous studies with limited taxon sampling have generated large amounts of partially overlapping sequence data for many species. Here, we combine these data and produce a novel estimate of extant amphibian phylogeny, containing 2871 species (40% of the known extant species) from 432 genera (85% of the 500 currently recognized extant genera). Each sampled species contains up to 12,712 bp from 12 genes (three mitochondrial, nine nuclear), with an average of 2563 bp per species. This data set provides strong support for many groups recognized in previous studies, but it also suggests non-monophyly for several currently recognized families, particularly in hyloid frogs (e.g., Ceratophryidae, Cycloramphidae, Leptodactylidae, Strabomantidae). To correct these and other problems, we provide a revised classification of extant amphibians for taxa traditionally delimited at the family and subfamily levels. This new taxonomy includes several families not recognized in current classifications (e.g., Alsodidae, Batrachylidae, Rhinodermatidae, Odontophrynidae, Telmatobiidae), but which are strongly supported and important for avoiding non-monophyly of current families. Finally, this study provides further evidence that the supermatrix approach provides an effective strategy for inferring large-scale phylogenies using the combined results of previous studies, despite many taxa having extensive missing data.

现生两栖类是陆生脊椎动物中多样性最为丰富的演化辐射支系之一，已知现存物种数量超过6800种。尽管近年来学界对其保护生物学、物种分化与分类学研究投入了大量关注，但此前已发表的该类群系统发育（phylogeny）研究中，涵盖的物种数均未超过522种。然而，诸多受限于类群取样规模的研究，已为大量两栖类物种积累了大量部分重叠的分子序列数据。本研究整合上述数据，构建了全新的现生两栖类系统发育估计树，共涵盖432个现生属（占当前已确认的500个现生属的85%）下的2871个物种，占已知现生两栖类物种总数的40%。每个采样物种均可获得来自12个基因（3个线粒体基因、9个核基因）的最多12712个碱基对（bp）序列，单物种平均序列长度为2563个碱基对。本数据集为此前多项研究确认的诸多类群提供了强有力的支持证据，但同时也揭示多个当前公认的两栖类科并非单系群，其中以雨蛙总科类群（hyloid frogs）尤为显著，例如角蛙科（Ceratophryidae）、圆口蟾科（Cycloramphidae）、细趾蟾科（Leptodactylidae）以及攀蛙科（Strabomantidae）。为修正上述分类问题及其他相关不足，我们针对传统上以科和亚科为分类等级界定的现生两栖类类群，提出了修订后的分类系统。这一新分类体系包含多个当前主流分类系统未予认可的科，如阿尔多蟾科（Alsodidae）、巴奇蟾科（Batrachylidae）、鼻角蟾科（Rhinodermatidae）、齿蟾科（Odontophrynidae）以及泽蟾科（Telmatobiidae），这些类群均得到了强有力的系统发育支持，且对于避免当前各科出现非单系群问题至关重要。最后，本研究进一步证实，尽管诸多类群存在大量缺失数据，但采用超级矩阵（supermatrix）法整合既往研究结果以构建大规模系统发育树，是一种行之有效的研究策略。